Development of SNP Markers to Distinguish Various Watermelon Traits and Validation Using Fluidigm Genotyping Assay

Sang-Min Yeo(Sang-Min Yeo),Jeong-Eui Hong(Jeong-Eui Hong),Md Abdur Rahim(Md Abdur Rahim ),Saleh Ahmed Shahriar(Saleh Ahmed Shahriar ),Phillip Choe(Phillip Choe),Sun-Kyun Jung(Sun-Kyun Jung),Ill-Sup No 한국육종학회 2023 Plant Breeding and Biotechnology Vol.11 No.2

Watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] is one of the economically most important fruit crops of the Cucurbitaceae family. Among different watermelon traits, disease resistance and fruit quality are the important traits for growers and consumers. The single nucleotide polymorphism (SNP) markers similar to those traits can potentially and cost-effectively distinguish the genetic variations among these traits. Consequently, we developed 33 SNP makers linked to different watermelon traits associated with fruit quality and disease resistance, and validated in the genetic resources of watermelon and F1 breeding lines using ‘Fluidigm SNP Genotyping’ assay. Most of the SNP markers distinguished the alleles into three different types such as reference allele, alternative allele and heterozygous from watermelon genotypes for various traits. The SNP markers ‘ZymFL-T81P’ (ZYMVresistance), ‘FON1-U161’ and ‘FON1-S075’ (Fusarium wilt-resistance), ‘Pmr21-Cla831’ (PM-resistance), and ‘ClGBS-J168’ and ‘GBS-GC230’ (GSB-resistance) can successfully differentiate resistant (R), susceptible (S) and heterozygous watermelon genotypes. Similarly, the SNP marker associated with sugar content, citrulline content, arginine content, rind hardness, flesh firmness, fruit shape, rind strip pattern of watermelon fruit and seed coat colour can successfully distinguished the watermelon genetic resources and F1 breeding lines as reference allele (A) type, alternative allele (B) type and heterozygous (H). These SNP markers could be utilized for marker assisted selection as well as screening of a large number of watermelon germplasm for fruit quality and disease resistance. However, further validation like artificial inoculation of pathogens for the traits related to disease resistance is required in watermelon crops.

Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

Kang, Jin-Ho,Yang, Hee-Bum,Jeong, Hyeon-Seok,Choe, Phillip,Kwon, Jin-Kyung,Kang, Byoung-Cheorl Korean Society of Horticultural Science 2014 원예과학기술지 Vol.32 No.4

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

Jin-Ho Kang,Hee-Bum Yang,Hyeon-Seok Jeong,Phillip Choe,Jin-Kyung Kwon,Byoung-Cheorl Kang(강병철) 한국원예학회 2015 한국원예학회 학술발표요지 Vol.2015 No.5

Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

Jin-Ho Kang,Hee-Bum Yang,Hyeon-Seok Jeong,Phillip Choe,Jin-Kyung Kwon,Byoung-Cheorl Kang 한국원예학회 2014 원예과학기술지 Vol.32 No.4

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang F1-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

Relative impact of amyloid-β, lacunes, and downstream imaging markers on cognitive trajectories

Kim, Hee Jin,Yang, Jin Ju,Kwon, Hunki,Kim, Changsoo,Lee, Jong Min,Chun, Phillip,Kim, Yeo Jin,Jung, Na-Yeon,Chin, Juhee,Kim, Seonwoo,Woo, Sook-young,Choe, Yearn Seong,Lee, Kyung-Han,Kim, Sung Tae,Kim, Oxford University Press 2016 Brain Vol.139 No.9

<P>Amyloid-beta deposition and cerebral small vessel disease are major contributors to age-related cognitive decline. In a longitudinal study of mild cognitive impairment, Kim et al. show that amyloid-beta and lacunes have differing effects on cognitive trajectories. Amyloid-beta has a greater impact on memory, and lacune number on frontal-executive function.Amyloid-beta and cerebral small vessel disease are the two major causes of cognitive impairment in the elderly. However, the underlying mechanisms responsible for precisely how amyloid-beta and cerebral small vessel disease affect cognitive impairment remain unclear. We investigated the effects of amyloid-beta and lacunes on downstream imaging markers including structural network and cortical thickness, further analysing their relative impact on cognitive trajectories. We prospectively recruited a pool of 117 mild cognitive impairment patients (45 amnestic type and 72 subcortical vascular type), from which 83 patients received annual follow-up with neuropsychological tests and brain magnetic resonance imaging for 3 years, and 87 patients received a second Pittsburgh compound B positron emission tomography analysis. Structural networks based on diffusion tensor imaging and cortical thickness were analysed. We used linear mixed effect regression models to evaluate the effects of imaging markers on cognitive decline. Time-varying Pittsburgh compound B uptake was associated with temporoparietal thinning, which correlated with memory decline (verbal memory test, unstandardized beta = -0.79, P < 0.001; visual memory test, unstandardized beta = -2.84, P = 0.009). Time-varying lacune number was associated with the degree of frontoparietal network disruption or thinning, which further affected frontal-executive function decline (Digit span backward test, unstandardized beta = -0.05, P = 0.002; Stroop colour test, unstandardized beta = -0.94, P = 0.008). Of the multiple imaging markers analysed, Pittsburgh compound B uptake and the number of lacunes had the greatest association with memory decline and frontal-executive function decline, respectively: Time-varying Pittsburgh compound B uptake (standardized beta = -0.25, P = 0.010) showed the strongest effect on visual memory test, followed by time-varying temporoparietal thickness (standardized beta = 0.21, P = 0.010) and time-varying nodal efficiency (standardized beta = 0.17, P = 0.024). Time-varying lacune number (standardized beta = -0.25, P = 0.014) showed the strongest effect on time-varying digit span backward test followed by time-varying nodal efficiency (standardized beta = 0.17, P = 0.021). Finally, time-varying lacune number (beta = -0.22, P = 0.034) showed the strongest effect on time-varying Stroop colour test followed by time-varying frontal thickness (standardized beta = 0.19, P = 0.026). Our multimodal imaging analyses suggest that cognitive trajectories related to amyloid-beta and lacunes have distinct paths, and that amyloid-beta or lacunes have greatest impact on cognitive decline. Our results provide rationale for the targeting of amyloid-beta and lacunes in therapeutic strategies aimed at ameliorating cognitive decline.</P>

Soft, thin skin-mounted power management systems and their use in wireless thermography

Lee, Jung Woo,Xu, Renxiao,Lee, Seungmin,Jang, Kyung-In,Yang, Yichen,Banks, Anthony,Yu, Ki Jun,Kim, Jeonghyun,Xu, Sheng,Ma, Siyi,Jang, Sung Woo,Won, Phillip,Li, Yuhang,Kim, Bong Hoon,Choe, Jo Young,Huh National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.22

<P>Power supply represents a critical challenge in the development of body-integrated electronic technologies. Although recent research establishes an impressive variety of options in energy storage (batteries and supercapacitors) and generation (triboelectric, piezoelectric, thermoelectric, and photovoltaic devices), the modest electrical performance and/or the absence of soft, biocompatible mechanical properties limit their practical use. The results presented here form the basis of soft, skin-compatible means for efficient photovoltaic generation and high-capacity storage of electrical power using dual-junction, compound semiconductor solar cells and chip-scale, rechargeable lithium-ion batteries, respectively. Miniaturized components, deformable interconnects, optimized array layouts, and dual-composition elastomer substrates, superstrates, and encapsulation layers represent key features. Systematic studies of the materials and mechanics identify optimized designs, including unusual configurations that exploit a folded, multilayer construct to improve the functional density without adversely affecting the soft, stretchable characteristics. System-level examples exploit such technologies in fully wireless sensors for precision skin thermography, with capabilities in continuous data logging and local processing, validated through demonstrations on volunteer subjects in various realistic scenarios.</P>